No, this is a fresh install of 3.0.1, checked out from the 3.0.1 SVN tag.

Also, just tried it on a freshly setup subdomain site - same issue.

I'm also missing the option to enable plugins for *individual* sites, all i now can do is to auto-enable plugins and (presumably) give the user the choice to activate a certain plugin - which is the menu entry i'm currently missing =)